Doctor Whooves 1: Shadows of ponyville
by Laura Heartstrings
Summary: Derpy Hooves is having an ordinary day, That is, until she receives a mysterious journal, containing Pinkie Pie's adventures with a mysterious stallion named the Doctor. The TARDIS crashes into Sugar cube corner,and the Doctor has regenerated into a pony, But he is not the only thing to have crossed through the rift, one of the Doctors old foes, the Vastha Nerada have also come.
1. Prologue

Derpy hooves fluttered through the rain. It had been a hard day delivering letters and packages to the citizens of Ponyville, and she was ready to get home. "Derpy!" the urgent cry cut through the rain that had poured heavily throughout the day. She sighed. _Probably some urgent letter somepony forgot to post this morning. _When she saw Twilight sparkle, Derpy got confused. All of the princesses letters were dealt with by Spike. "Derpy." Twilight sighed with relief "Here, this is for you." She handed Derpy a brown, rectangular package with a note tapped on it. "The note will explain every thing." Derpy studied the package "what is…" she looked up and Twilight was gone "where…" she blinked. Shrugging, Derpy placed the package in her satchel and took of towards her home.

Derpy pushed open the door to her house. "I home!" she called.

"Mommy!" Dinky squealed "You're finally back!"

"Yep, I'm back! What did you do today?"

Dinky shrugged "Nothing really, I just drew some pictures."

"Where's Sparkler?"

"Still out." A voice called for the kitchen. Derpy's roommate, Carrot top poked her head out "She should be back in an hour or so.

"Thanks. I'll be in my bed room, Okay?"

"Bye!"

Derpy fished the package out of her bag. _The note will explain everything. _Twilight had said. Why had she disappeared right after giving her the package? Derpy open the note.

_Dear Derpy_

_As I write this, one thing is clear. Neither of our lives will ever be the same. This journal should send you all of my adventures with a mysterious stallion named the Doctor. The first one starts today, but do not under any circumstances attempt to ask me about this journal. Do not let this book get into harms way. Do not let anypony see it. Each story should come to you when it needs to. And no matter what anypony tells you, please do not believe for one second that the Doctor caused the upcoming problems. He saved thousands of pony's lives; don't let anypony tell you otherwise._

_These all really happened, but you're the only pony who can know about them, for now_

_~Pinkie Pie_

Derpy stared at the note for a few seconds, letting it sink in. Why would Pinkie trust her with something so important? And why did Twilight give it to her, and not Pinkie? It didn't seem like a joke, it seemed too real to be a joke. In the package there was a red journal. Derpy opened the journal and for a second of bitter disappointment, there was nothing there. Then the words faded onto the page.

_Adventure 1: The Shadows of Ponyville_

"The Doctor." Whispered Derpy. "Doctor who?"


	2. A Box from the Sky

"There, four blueberry muffins, as usual." I put the bag on the counter.

"Thanks Pinkie, you guys make the best muffins here." Sparkler said as she placed the coins on the table.

"Thanks! Tell your mom I said hi!" I skipped around to the kitchen "Gummy! What are you doing in there?"

He gave me a look that seemed to say "I got bored."

I rolled my eyes "Come on Gummy, out of the flour." I picked him up. I put him on the floor out side of the kitchen. He shook and the flour went everywhere.

"You do realise that now I'm going to have to clean that up right?

The alligator looked at me "Soz bro."

"Just checking"

I looked around the deserted bakery. The Cakes went to Manehatten for a vacation, and most ponies didn't want to go anywhere in the rain, so me and Gummy were alone.

"You know what I think Gummy?"

He blinked "Enlighten me."

"We should have a party soon! One even better than the last few!"

"Yes, we should, but this time we should most definitely put more sugar in punch, last time we did not quite put enough in."

"Yeah, you're probably right."

Suddenly a loud sound started up

"What's that?" I looked around. Nothing. My tail started twitching.

"Something's gonna…" A blue box appeared from out of nowhere, tumbling around before crashing into the ground.

"…Fall." I finished as the dust settled. A chestnut stallion in a tweed jacket staggered out of the box.

"Fingers, Fingers, no fingers." He said before letting out a puff of gold dust and collapsing.

"Are you okay?"

Gummy poked his head out of the rubble.

He then latched onto the stallions head

I really wasn't sure what to do next at this point. A blue box that made weird sounds had appeared in Sugar cube corner, demolished the floor, and a strange stallion that I had never seen before staggered out of said box. I decided that I would move the stallion, which was easier said than done.

First of all, I had to get Gummy of him. And Gummy did NOT want to let go. Then I had to decide where to move him, first thought about putting him on the couch upstairs. So, I rolled him out of the rubble and attempted to push him up the stairs. It didn't work, so I tried dragging him up the stairs, again, it didn't work. Basically I couldn't get him up the stairs.

Then I tried to slump him in a chair. He rolled off. In other words, it was really hard to get him around. Eventually I got the mysterious stallion half on a table, half on a chair. Gummy had managed to get hold of his leg.

I giggled "Silly Gummy, get off his leg!"

He looked at me "No."

"Gummy get off his leg."

"No."

"Gummy…"

"What?"

"Let go of his leg. Now"

He stared at me for a second then let go. "Fine, but you owe me one Pinkamena."

I rolled my eyes "Thank you."

I looked at the blue box. I had cleaned up the mess earlier, and the box was just sitting in small crater it had made. There was a sign on the door.

"Pull to open." I read aloud

"Open it! Open it! Open it!" Gummy bit my tail.

"Alright, Alright! I'll open it!" I giggled.

I pulled, it wouldn't open. I pulled again, harder this time, but it still wouldn't open.

"It's locked." I told Gummy.

"There's probably a key in his pocket!"

"Gummy, I am not going through somepony's jacket."

"Thought it was worth a try."

I skipped into the kitchen where I started making a cake.

"I'm home!" Sparkler called from the next room

Derpy jumped. She didn't realise that she had been reading for so long. She was about to get up when she remembered Pinkie's instructions _Do not let anypony see it._

The mail mare placed a lean tissue on the page she was on and slid the journal under her pillow. She then trotted out into the living room, embracing her adopted daughter in a hug.

"hello my little muffin, how was your day?"

"Good" the purple unicorn said handing Derpy a brown paper bag "Pinkie Pie says hello."

Derpy thought back to the first part of the book.

"Did you hear anything…, Odd after you left sugar cube corner?"

Sparkler thought for a moment "Come to think about it, yes. Why?"

Derpy giggled nervously "no reason."

She looked at her mother with concern "okay then."

The grey Pegasus trotted back into her room. _Sparkler heard something! Could she have heard…?_ Both of Derpy's eyes rested on the pillow


	3. Stay out of the Shadows

The next fifteen or so hour's were kinda boring, made a cake, played with Gummy, went to sleep, woke up, and stared at the stallion for a while drinking my Dr. Hay. Finally, around 8.15ish he came to.

"Gaah! Hands! No hands! Or feet, where did my shoes go! My face feels kind of…" he started feeling his muzzle "I'm a horse!"

"Hi!" I bounced up to him "I'm Pinkie Pie!"

"Aah!" he fell off his chair. He sat up rubbing his head "where did you come from?"

"Duh, I've been sitting here for hours!"

"Why?"

"Well you've been out cold for fifteen or so hours, I was making sure you weren't dead."

"Right… Where am I?"

"Sugar cube corner!"

His face was blank

"In Ponyville."

Still blank

"Near Cloudsdale…"

Blank as a canvas.

"How can you not know where Cloudsdale is?"

"Hate to be rude but, Pinkie wasn't it?"

I nodded

"Pinkie have you seen a blue box anywhere?"

"You mean the one that crashed into the floor yesterday?"

"Probably, yes."

"Right there!"

He paused for a moment.

"You're a pony."

"Umm… yeah…"

"This is a bakery…"

"Yes…"

"You work here?"

"Yeah, why?"

He grinned "a pony that works in a bakery! That just brilliant!"

I looked at him "Are you okay?"

"Yeah I'm fine… but do you have any blueberry muffins? I'm famished!"

"Sure!"

I skipped to the kitchen, on the way I passed Gummy

He looked at me "that guy is a total Whack job."

"Gummy, don't be rude." I scolded

I put a muffin on a plate and carried it to the table. When he got the muffin to him, he devoured it quickly without even picking it up. Then he paused again.

"How did you make this?"

I giggled "why do you keep asking silly questions?"

"Well this is my first non-humanoid regeneration, it's very exciting!"

I looked at him "Non-humawhatta?"

He shook his head "Never mind, Thank you for the muffin." he said getting up, attempting to stand up on his hind legs, than falling over.

"Are you okay?"

"Yep I'm fine" he said getting up again. "I'm fine."

"Hey I didn't catch your name."

"Oh sorry, I'm the Doctor."

"Doctor who?"

"Just, the Doctor."

"Oki Doki Loki! Welcome to Ponyville, Doctor!"

"Thanks."

He walked towards his box.

Then all of a sudden, we heard somepony scream.

"Someponies in trouble!" I ran towards the door "Are you gonna come?"

Then, for no apparent reason, he started to look sad "I promised myself I wouldn't help anymore."

"Right then, well I'm going." I say starting to run out the door.

I don't know when but eventually he started to follow me.

"I thought you said you didn't help."

"I'm not. Just, investigating."

We ran towards the source of the noise. Eventually we found it, there, in city square, was Pipsqueak, and he was being corned by two skeletons.

"Oh no." the Doctor muttered

"Pip!" I exclaimed

The Doctor shoved his muzzle in his coat pocket, producing a slim metal object with a green light at the tip. He pressed the button, causing it to make a whirring sound. He then examined the device with wide eyes.

"Oh no." he repeated.

"What's that thing?"

"Sonic screwdriver. I'll explain later, but Pinkie?"

"Yes?"

"Stay out of the shadows."


	4. The Problem with Hooves

The crowd was in absolute chaos, we had the ponies who were attacking the skeleton, the ponies who were Panicking and screaming, and running. And then there were the ponies that were trying to find out what was going on, caught up in the turmoil.

"What do you mean?" I asked him

"It's the Vastha Nerada, microscopic beings that… Is that a unicorn?"

"What? Yes it's a unicorn, why?"

"Well, there are no unicorns or Pegasi for that matter, where I come from."

"Where are you from, another planet?"

"Well, yes actually."

"That explains a lot. What were you saying?"

"Umm… oh yes, Vashta Nerada, microscopic beings the live in the shadows. Tear the flesh of their victims in a second."

"Oh. Cheerful. So how do you get rid of it?"

"Well, like I said they live in the shadows, and absolutely hate light. Nothing like this has ever happened before?"

I shook my head "A lot of things have happened here, but never walking skeletons."

The Doctor shoved his muzzle in his coat pockets "I know there in her somewhere… Ah ha!" he exclaimed pulling out a pair of 3D glasses and placing them on his hooves. He then attempted to get them on by shoving his nose in the lens, all the brown stallion managed to do was knock them on the ground

"Darn it!"

Then he tried to scoop them up with the top of his hooves, it didn't work.

"Do you need some help?" I asked picking them up.

He looked at my hoof "How did you do that?"

"Do what?"

"Pick that up!"

"That's a silly question!"

"You have no fingers!"

"What does that have to do with anything?"

"That has everything to do with picking up stuff!"

"Do you want them or not?"

"Oh, umm ...Yes thank you."

He put the glasses on "Aha! I thought so!"

"What?"

He gave me the glasses "look through these."

I put them on "whoa!" on the bones I could see some, well, stuff is the only way to describe it.

"What is that?"

"Void stuff. There is a whole bunch of different universes, differing from each other in key aspects, and between them is a void, a huge gap of nothingness."

I nodded "Right…"

"Void stuff is stuff in the void that clings to whatever passes through it. Now, considering that Vashta Nerada is from the same universe that I come from that means I passed into another dimension where the main template for life forms is equine not humanoid! Oh this is just brilliant!"

He looked like a little foal opening their Hearths Warming Eve presents.

"So... You're from another universe?"

"That's about right Ms Pie."

"And the void stuff is on the stuff that turns ponies into walking skeletons?"

"Yes."

"So we can see where it is?"

"I guess so, why?"

"It's coming right towards us."

A skull piercing hiss started up._ Doctor…_

"I can see why that could be a problem."

"What do we do?"

"Well basically, run!"

"Sounds good."

We started off towards sugar cube corner, but the Doctor kept tripping on his pants, eventually he just gave up and took them off.

"I cant run in these things, not as a pony anyways."

"You know it's kinda funny."

"What?"

"I've never actually seen anypony wearing pants before."


	5. Bigger on the Inside

The skeletons followed in pursuit.

"I thought those were destroyed!"

"I told you, they can devour their preys flesh in less than a second! Their probably different ponies!"

"So, where are we going?"

"You'll see!"

"**_Doctor…_**"the skeletons hissed.

"Wait a minute, that skeleton is talking…" I said.

"Yes it is!"

"Im pretty sure Skeletons can't talk."

"It's not the skeletons; it's the Vashta Nerada, the sonic screwdriver picked up some kind of energy, which is probably what's enabling them to talk."

"The sonic screwdriver? That is the second time you mentioned that."

"Again, I'll explain later." He grinned

"What?"

"I've missed this."

"Missed what?"

"Running."

"Oki Doki Loki?"

"**_Doctor…"_**

"Right. Skeletons."

We charged down the street, back into the bakery. Once we were in, the Doctor headed straight for the blue box.

He poked his head out "you coming?"

"Coming where?"

"In here."

"Why?"

"Trust me on this."

I looked at him, and then walked towards the box.

"So what's…?"

I stopped dead. Inside the box, there was a room, a room to big to fit in a box that small. In the middle there was a table with lots of different knob's and switches on it, and was supported by a glowy tubey thingy that stretched right up to the ceiling, up to three rings with circular symbol's on them. It seemed dark in there, and the orange lights didn't illuminate much, but the blue lights glowed brightly. There were stairs leading into a hallway, and the edges of the platform in the centre were lined with Railings.

"Go on, say it. Everyone does."

"It's huge!"

He grinned "It's called the TARDIS, it can travel anywhere in time and space."

The skeletons banged on the door.

"So why are the skeletons after you?"

"I don't know! There are lots of reasons for things to be chasing me!"

"What do you mean?"

"I travel through time and space, I…"

"**_DOCTOR!_**" the skeletons rasped.

I turned to the Doctor "Why are you showing this to me?"

"Well, you deserve it; I did demolish your floor."

The skeletons banged on the door.

"What are we going to do about those skeletons then?"

"You tell me." The stallion replied, walking towards the table.

I popped up in front of him "Well there has to be some reason we ran into here."

He blinked, startled at me jumping up in front of him

"what if theres not, what if im a complete moron?"

"Then I think were doomed." I said bouncing around the room. "But I don't think you're a moron so as I was saying you said that the Vashta Nerada stuff doesn't like light so were here for some bright lighty thingy."

"Absolutely spot on Ms Pie!"

"Why do you keep calling me miss pie silly?"

"Well I…"

"**_DOCTOR!_**" The voice outside rasped.

"Alright pinkie, we'd better get a move on!"  
A few seconds later he emerged with a contraption that looked kinda like a speaker on wheels

"Our bright lighty thingy! Sometimes I wonder why I even have some of this stuff stored back there."

"Great! Now what?"

"Now we talk to them!" He walked up to the door

"**_DOCTOR…_**"

"Oi, Quit your shouting, we can hear you perfectly fine; now what do you want?"

"**_We have been let into this world, and promised a whole new source of food, and you are the only threat."_**

"Well its not like I'm going to just walk out there to my doom is it?"

They fell silent

"That being said it's not like I'm just going to sit here and let you destroy this town, so you have two options, Go back to eating road kill, and leave this species alone, or I will make you."

The skeletons lashed out at the door.

"I think that's a no." I said.

"Yeah, Probably. Listen you have one more chance."

"**_The shadows of Ponyville will block out even the sun._**"

"I'm warning you…"

The skeletons hissed.

"Have it your way then." The Doctor burst out the door, pushing the device in front of him "GERONIMO!" he shouted, slamming down the big red button on the top.

"Poptrots that's bright!" I exclaimed shielding my eyes.

The skeletons screamed in agony, it was a terrifying, horrific, bloodcurdling scream that I don't think I could ever forget.

I blinked as the light faded. There were two piles of bones straight outside the doors and standing over them was a very grim looking Doctor.

"What's wrong?

"They said they've been let into this world."

"So who let them in?"

"Exactly, I think we need to figure that out." He grinned

"What did they say about the shadows of Ponyville again?"

"Well, that they would block out the sun, but how would they block out the sun unless..."He trailed off

"Unless?"

"Unless a lot of Vashta Nerada clumped together and formed a giant shadow."

"Can they do that?"

"I don't know."

I saw something move outside. "Umm… Doctor?"

"Yeah?"

"I think we have some more visitors."

"Right then, we'd better deal with those."

So, we went outside, blasted the skeleton, and then what were we greeted by? Five more skeletons spaced out down the road. And they didn't look very happy. Granted can skeletons even look happy? I never had any reason to think about think it before. I mean, they're bones, so they kind of stay the same, and they don't have eyes. they're really just, hollow I guess. My point is that the skeletons were looking at us and were about to attack.

"Pinkie?"

"Yeah?"

"Get on the light."

"What?"

"We are going to roll down the street."

"Oki doki loki?"

"Let's just say I have no idea why this thing has an engine." He said as we jumped on top of it. "You might want to hold on!"

We charged down the street. It was awesome; going straight past the Vashta Nerada infected skeletons on a incredibly fast, bright light that for some reason had a motor and wheels. Actually it was probably one of the strangest things I had ever done, and that's saying something!

Of course, The Doctor was really bad at driving it.

"Are you sure you know how to drive this thing?"

"Well, it probably isn't meant to be driven with _hands_, let alone hoofs, then again I don't actually know what it's for anyways so…"

"Well then, it can't be any worse if I drive. Scot over."

"What?"

"No offense, but your kinda incompetent with your hoofs. Look out!"

We swerved violently, just avoiding becoming pancakes on a wall.

"Do you even know how to drive this thing?" I asked

"Not really! Do you?"

"No!'

I looked around, behind us all of the skeletons weren't moving, probably because of the lighty thingy, but it seemed like the shadows were following us.

"Cutie mark crusaders! Skeleton fighters!"

"Doctor, stop the thingy magig!"

"Why?"

"Those three little fillies will be in serious trouble if we don't stop them!"

He nodded and turned around

"Wait a minute; please tell me you can stop this thing."

"Well…"

"Never mind, I'll tuck and roll!"

They shrieked when I appeared out of nowhere.

"Oh hi Pinkie!" exclaimed Sweetie belle

An idea popped into my head "hey girls, can you pretty please with sprinkles on top ask your sisters, Rainbow dash and Fluttershy to meet me at Twilight Sparkles house?"

"Umm, ah guess so." Said Apple bloom

"Sure!" The little unicorn nodded

"But we were just going to get our cutie marks in skeleton fighting!" objected Scootaloo

"Please! This is super duper important!"

A crash sounded down the street.

"That's one way to stop a lighty drivey thing!" the brown stallion called out.

"Please?"

"Alright…"

"Oh and another thing, stay away from the skeletons, and shadows. Stay out of the shadows!"

"But…" Apple bloom started

"Do you want to be part of a skeleton army of shadows after being devoured by thousands of microscopic beings in less than a second?" I demanded, shoving my face into the fillies.

"No…"

"Then stay away for the shadows and skeletons."

I skipped toward the wreckage of the bright lighty thing.

"Hey Doctor, are you alright?"

He nodded "been worse. Any luck with the fillies?"

"Yeah, now we need to get to Twilight Sparkles house, I'm really glad she hasn't moved back to Canterlot yet, that would make this very complicated."

"Make what complicated?"

"Saving the day!"

"How so?"

"I'll explain on the way."

We stared walking, a five minute walk at the most, possibly more if you included the detours we would have to make to avoid the darkest streets.

"It all started about three years ago, well; actually it started one thousand and three years ago when Princess…"

I stopped. In front of use were four skeletons that were slowly advancing on us!

"We don't have the light, okay, I've been in worse situations than this." The doctor said

I grinned "don't worry, I've got us covered!" I said whipping out the party canon.

"How… Where did that come from?"

"I never leave home without my party canon!" I declared, marching towards the walking dead.

With a direct shot, the first one fell apart easily, but then I had to avoid the shadow, a shadow that was coming straight towards me! Swiftly, I dodged one of the quick tentacles of darkness, a dodge that was quickly followed by a kick in the second skeletons rib cage. They hissed and lunged at me.

"Missed me!"

They lunged again

"Missed me!"

They lunged yet again

"Now you gotta kiss me!" I sang firing the party canon straight in their face! Now I was faced with a huge challenge. Well, a huge shadow anyways.

The Doctor lunged forward, welding his sonic screwdriver

"Oh no you don't!" His voice was muffled by the device in his mouths, but still, the shadows slunk back into their rightful places.

"Thanks!" I exclaimed turning towards the third one. This one was slightly more hesitant, and we circled each other a few times before it came charging at me. I slid underneath it, firing directly in its ribs.

The fourth skeleton was charging at full speed, with what used to be wings spread out uselessly. Just as they were almost upon me, I fired, and they blew apart like a poorly made cupcake!

"Tada!"

"Your canon fires confetti streamers and balloons, should I even ask?"

"It's for quick decorating if I need to throw an emergency party!"

"An Emergency party?"

"Yep!"

"Why would you…"

"**_The shadows of Ponyville will block out even the sun…"_**

It seemed to get darker all of a sudden, but that was nothing compared to what was coming.

"Oh cupcakes…" I almost whispered

All around, the shadows seemed to be climbing, forming a dome around the small town. Screams came up from the ponies that were still outside. There was a panicked flurry to get inside houses and find loved ones.

The Shadows of Ponyville had blocked out the sun.


	6. Derping in the dark

The room went completely dark. Derpy couldn't see a thing, not even the journal in front of her. It was Sunday, So she didn't have any work and she had planed to spend the whole day reading, her plans however, weren't going as smoothly as she had planned

"Well that's just great!" The grey Pegasus exclaimed. She had caught up with real time, and now she couldn't read what was happening.

"Derpy!" Carrot Top called out from the living room "are you ok?

"Yeah, Are the girls with you?"

"We're right here!" Sparkler Answered

"Alright listen to me, head down to the basement and turn on all the lights down there, alright?"

"Why, what's wrong?" Carrot top asked.

"Trust me! Head down to the basement and turn all the lights on down there! It's the only safe place in town!"

"What are you talking about?"

"Just trust me."

Derpy started to form another plan. She shoved the plate of muffins on her desk in her mail mare satchel, along with the journal, a flashlight (which she had tripped on and figured it would be useful.) and a tennis racket, Don't ask where she got the tennis racket from, It just sort of appeared on her desk earlier that morning, nopony actually knows how.

The Mail mare flew towards the door, only to crash into a wall, causing some picture frames on the other side if the wall to fall down and shatter. "Ow!"

Carrot top sighed, "This is why we can't have nice things."

"Sorry! I can't see in the dark!"

"Or at all." The earth pony muttered under her breath.

Finding the door Derpy Hooves hovered in the air above the living room, which was being illuminated by Sparkler, Dinky was trying to help, but she ended up just sending sparks everywhere.

"To the basement!" The Clumsy Pegasus announced, then proceeding to fall down the stairs. "Whoops."

Carrot top flicked the light switch on, and the three other ponies went down, no doubt in a more, shall we say, graceful style than Derpys. Once they were down Derpy flicked the switches to all the lights in the basement.

"Oh shoot! I need to go get something upstairs! I'll be right back, don't turn any of these lights off!"

"Alright Mommy." Dinky squeaked.

"What exactly did you forget?"

"Uh, something!" Derpy hurried up the stairs, not giving a chance for any more questions. When she got to the top of the stairs, The Pegasus slammed the door shut! Reaching for the key that was always left on the table, she locked it as well

"DERPY!" she could hear Carrot top stomping up the stairs. "Did you lock this door!" she jiggled the doorknob "DERPY HOOVES OPEN THIS DOOR RIGHT NOW OR YOU WILL BE IN FOR A WORLD OF PAIN!"

Rummaging through the drawer, flashlight in mouth Derpy found a pen and paper

"DERPY, DON'T MAKE ME BREAK DOWN THIS DOOR!"

Derpy wrote a note that read:

Ponies locked in basement

Please let them out

-Derpy Hooves

She placed the key on the note and took of into the air, crashing through the window "Uups!"

"DERPY!"

Ignoring her roommate's frustrated cries Derpy Hooves stood up and walked towards Sugar Cube Street, which was named for its famous bakery, Sugar cube corner.

If I can't read what's going on, I'll watch what's going on! She thought confidently.

When she arrived and the bakery, Derpy saw a green unicorn in a bathrobe and 3-D glasses examining a plie of bones. Looking up, the unicorn saw Derpy and walked up to her.

"Excuse me mam," she started, flashing a badge so fast that Derpy couldn't see what was on it. "But I am going to have to ask you to leave the premises immediately. Until further notice it will be under quarantine under the authority of the research institute of fractures in time."

"What?" Derpy Exclaimed, feeling extremely confused.

"You have to leave. Now."

"Why?"

"Because it's not safe for civilians at the moment!"

"And you're not a civilian?"

"No I work for…" she shook her head. "Look it doesn't matter right now, just, you have to leave the area, if you see any other skeletons do not touch them and immediately report them to me ok?"

"I think it matters who you work for if I'm going to have to report skeletons to you. I don't even know who you are for Celestia's sake!"

"I work for a top secret organization that nopony is supposed to know about called R.I.F.T. and I am supposed to get all civilians out of the area until everypony else gets here no if you would be so kind as to…" she frowned "wait a minute, everypony has gone into their house's or there friends houses or something like that, why haven't you?"

"Um, well you see I was just umm, I was trying to oh find … something and umm… I got… lost! Yes I got lost!"

The unicorn wasn't convinced "really? What were you trying to find then?"

"Umm, It's not really a what it's more of a…who, uh yes I was to find my friend, uh… doctor, um, Time Turner!"

The unicorn still wasn't convinced "Oh really? Because I've never heard of a doctor Time Turner."

"Ah, well that's because, umm, he's from uh, Fillydelphia! And he's visiting!"

"Oh really, how do you know him?"

"He's my… Cousin!"

"I thought you said he was your friend."

"Umm, yes but we're really… close cousins."

"Oh really?"

"Uh… yes?"

"So why again are you lying?"

"Well, I am looking for somepony, but they're not my cousin.

"Then who?"

"I have no idea."

"Then why are you looking for them?"

"Because, well, Because, Well, I, you see, umm… well I got this, package and it had a note and well, umm yeah…"

"A package?"

"It was a journal."

"Okay then, that really doesn't answer the question."

"What was the question?"

"Why are you looking for somepony you don't know?"

"Oh right well there was a journal… and it had this... story in it and… I was umm… investigating… and um… yeah…"

"Investigating what?"

"Stuff."

"Care to elaborate on that a bit?"

"No…"

"I have a feeling you know more than you're letting on."

"Probably."

"I'm afraid you're not allowed to leave till you give me this information."

"Two minutes ago you were telling me to leave the premises immediately."

"I suppose so but this is a matter of national importance if you are withholding information that could compromise the security of this area you could be arrested."

Derpy smiled "the stuff causing this darkness are these microscopic things called Vashta Nerada you thrive in darkness and turn ponies into skeletons and stuff and don't like light… and stuff."

The unicorn raised an eyebrow "and how do you know this?"

"I told you, there was this journal."

"Right, Later I'm going to have to question you further on this, what was your name?"

"Oh, I'm Derpy, Derpy Hooves. And you are?"

"Lyra Heartstrings. Now this area is still not safe so if you would please leave."

"Oh, yes, right." Derpy backed away as Lyra returned to examining the bones.

Taking off, Derpy followed the trail of bones. She passed the smouldering wreckage of the bright lightly thingy and took note of where Pinkie talked to the CMC. When she finally saw where Pinkie fought off the skeletons, she heard somepony talking.

"So why does everyone have tattoos on their butts?"

"You know that you talk really funny Doctor."

"What do you mean?"

"Well, you say everyone not everypony."

"So?"

"That's just kinda weird."

"And I'm guessing you also say anypony and nopony as well?"

"Bingo."

"Alright then!" the Doctor laughed.

Derpy got a good look at the pair for the first time. The Doctor was a brown stallion, just like Pinkie had said in the journal, and he wore a tweed jacket, Derpy couldn't quite take note of anything else, her eyes were going crooked. Oh no not now! She thought, flapping around clumsily in the air, then knocking over a stack of crates. Quickly, she dropped down, hiding behind the crates she didn't disrupt.

"I think we're being watched." The Doctor's voice dropped down to a whisper.

The two earth ponies slowly walked towards the source of the noise. Derpy cringed at her own clumsiness. Now they'll find me and ask what I'm doing here! And the letter told me not to ask let them know…

Suddenly a high-pitched screeching noise sound from the next street, followed by a loud crash.

The Doctor and Pinkie Pie looked at each other and as if by some unspoken agreement they took off away from Derpys hiding place.

Derpy let out her breath and crawled down the alley next to her. When she got out there was a skeleton waiting for her.

"Uh oh." She hovered slightly above the ground, back up slowly, with the skeleton pursuing in kind.

Derpy crashed in to a tree, causing a branch to fall and crush the skeleton with a sickening crush. The grey Pegasus flew back down the alleyway as fast as she could, armed against the shadows with only a flashlight.

When she got back to the crate stack she went in the direction she saw the Doctor and Pinkie go, turned around the corner. Something exploded in front of her and everything went black

Derpy woke up to the sound of birds chirping. Bright sunlight shone in her eyes. "What happened?" she asked, even though there was nopony there to answer. It was about midafternoon, and Derpy hadn't had anything to eat since the night before. Realising how hungry she was, the Pegasus took a muffin out of her bag.

So how did the Doctor and Pinkie get rid of the Vashta Nerada? Derpy wondered.

Continuing to eat her muffin, the mailmare pulled the journal out of her satchel and continued reading.


	7. Jimmy the bear

"I think we're being watched." The Doctor's voice dropped down to a whisper.

We crept towards the toppled crates, not sure what to expect, when a loud screeching noise started up in the opposite direction, followed by a gigantic crash and the sound of shattering glass.

Me and the Doctor looked at each other, nodded, and ran towards the noise, turned the corner and bam! There was a huge bear thing with gigantic claws and these wings that stretched across the entire street! It was throwing around whatever it could reach and smashing stuff on the ground, shattering windows and cracking the street open!

Oh yeah and it was also on fire.

"What is that?" the Doctor asked me

"Oh, you know, its Fluttershys friend, Jimmy!" I joked.

It knocked of the whole second story of a building, sending fiery debris everywhere!

"Yes, because he looks incredibly friendly!" The Doctor said, dodging a heap of flaming wood.

Jimmy flipped a cart over blocking our entrance and blowing back a grey Pegasus that was walking down the street.

"Well, we're trapped!" I announced, ducking out of the path of a lamppost Jimmy sent my way with one of his high pitched roars.

"That we are Miss Pie!"

"Again with the Miss Pie?"

"You're bringing this up now?" some more stuff that was on fire flew above our heads.

"Well you're the one who keeps calling me miss pie, for Celestias sake, just call me Pinkie!"

Jimmy was getting pretty mad about not being able to hit us with anything, so he was squatting down, getting ready to jump on us!

"Look out!" I cried. The Doctor leapt out of the way and I did a really Impressive survival roll, if I do say so myself.

Jimmy let out a bloodcurdling screech, bending down and roaring in my face. And let me tell you, his breath smelled really bad.

I quickly slipped under Jimmy, and ran across the street towards a blue house

Now it was the Doctors turn to deal with Jimmy.

Jimmy dug his claws into the broken cement and heaved upwards, sending showers of flaming concrete and broken glass everywhere e. Now that I think about it though, I'm not sure how the concrete was on fire, but it was.

Jimmy was getting visibly frustrated and was trying to catch the Doctor between his front paws, but he was too quick for Jimmy. Eventually Jimmy gave up that and just sent fireballs at him.

"My tail is on fire!" he shouted, performing an incredibly funny looking dance to try and put it out, meanwhile Jimmy was about to bring his huge paws down and squish the Doctor.

"Look out!" I called. He rolled out of the way, finally succeeding in putting out the fire, and ran towards me. "In here!" I opened the door to the house. Jimmy tore the roof off the house, and we ran towards the back of the now burning building. The rafter collapsed as Jimmy ripped open the front of the building, and we narrowly avoided being crushed by the burning wood.

"Over there, there's a gap!" The Doctor rushed towards it

"Hurry up!" Jimmy was starting to throw things again. I coughed.

Once we navigated our way out of the burning wreckage we were back on the open street.

"Do you still have the glasses?"

"Yeah, why?"

"Because with them we can see the Vashta Nerada, It's the only way we can see if someplace is safe or not."

"Right." I put them on.

"Where did you pull those out of?"

"This streets alright, except for over there." I gestured towards a large tree. "There are a lot of them there."

We ran down to street, avoiding the little patches of vashta Nerada that showed up. Behind us I heard a high pitched roar. A very angry high pitched roar. A high pitched roar that seemed to say some very mean things such as I will skin you alive and I fart in your general direction. I think you get the picture.

We turned the corner. "Here!" I dived into a small gap between buildings. Jimmy marched straight passed our hiding place

"Nice place. Bit cramped."

"Meh. Does the job. As long as we're quiet we shouldn't be found."

"Right." There were a few moments of silence.

"So you're from another universe then?"

"Yeah, that seems to be the case."

"Travel between universes often?"

"Well, travel between universes is impossible; every time you do it the very fabric of reality is unravelled."

"So not much then?"

He laughed "not that often no."

"Then how did you get here?"

"Well, I don't actually know, I guess the TARDIS just kind of, slipped. But usually when a TARDIS is in another universe it loses all its power, but she's absolutely fine."

"And you're sure it's in another universe?"

"Positive. I have travelled through time and space for hundreds of years and I have never heard of colourful ponies with tattoos on their flanks. Also The TARDIS can't find earth anywhere."

"Earth? You mean like, Earth ponies, Dirt, the ground."

He shock his head "Earth is a planet in the milky way galaxy."

"Never heard of it." There were a few moments of silence "So are you from Earth."

More silence.

"No but I visit it a lot."

"Then where are you from?"

Even more silence. "I'm a time lord from the planet Gallifrey in the constellation Kasterborous."

And yet even more silence. "Wait a minute" a thought struck me "You said that you have travelled through time and space for hundreds of years..."

"Yeah."

"How old exactly are you?"

"Oh, lets see about one thousand, two hundred and sixty four."

"Oh, okay then."

He grinned "So what was this town called again? Ponyville?"

"Correctamundo!"

"What Planet and year?"

"couldn't your TARDIS tell you that?"

He shock his head "Insufficient data, the TARDIS doesn't know anything about this universe."

"Right. Well this planet's called Gaia and the year is 1126."

"Thanks."

"Also why does everyone, err, sorry everypony have a tattoo on their flank?"

"What, you mean cutie marks?"

"Um, yes."

I frowned "how do you not know about cutie marks if you have one?"

"What do you mean?"

"Look!" I gestured towards the hourglass on the Doctors flank.

"Huh, would you look at that! So what exactly is a cutie mark?"

"A pony earns his or her cutie mark when they discover their special talent, destiny, something."

"What."

"Like mine is for throwing parties!"

"Right, balloons"

"You said that you didn't help anymore, why not?"

Now he was sad "Well I've travelled for a very long time, and well, I've lost so much. My Best friends had just died and I was tired of losing everyone I loved, so I was going to park the TARDIS up on a cloud and just let the world pass around me but, somehow I ended up here."

"Oh…"

And let me tell you, there was quite a bit of silence after that.

"One more question." I said

"And what would that be?"

"What is the sonic screwdriver?"

"Well it…"

There was a moan followed by a giant crash. We peeked out of the alleyway. On the ground was Jimmy, the flames on his fur shrinking down to ashes.

In the opening to the next street was a cream Pegasus wearing 3D glasses and holding a dart rifle, he backed away into the darkness.

"Who was that?" the Doctor asked

"I have no idea…"


	8. Shadows underground

"Well okay then."

An idea was forming in my head "hey Doctor, you have a lot of different thing in your big blue box right?"

"Yes. why?"

" If there was something in there that could hack into Ponyvilles main power supply then we could send a giant surge of electricity through out the town causing all the lights to turn on brighter than they normally could then boom! No more Vashta Nerada!"

The Doctor smiled "I have just the thing!" he whipped out the sonic screwdriver

"So the sonic screwdriver hacks into things? But then how did it tell you that they were vashta Nerada? Are vashta Nerada like little computers design to eat things? Did you make them? Is this your fault? But why would you make microscpic computers designed to eat things? Maybe you were trying to get rid of something! But what? I know! there was something really bad that was eating all of your stuff So you designed the Vashta Nerada to eat it but then they went hay wire and killed your best friend so you followed them to this universe to destroy them it all makes sense now!"

"What? No! the sonic screwdriver can also scan things! It can hack into computers and things but that's not the only thing it does!"

"So the Vashat Nerada aren't robots?"

"No!"

"You sure?"

"Yes!"

"Oh. So…" I was interrupted by a brown hoof in my mouth.

"I'm just going to stop you there. The Vashta Nerada are completely independent creature that were not created by anyone. Pony. Alright?" I nodded "Now do you know where you can access Ponyvilles main power supply?"

I nodded "id om mham stphreet tafe a rirft am fem you took a…" he pulled his hoof out of my mouth "Thank you! Now follow me!" I skipped down the street."

We raced down the streets, not running into any skeleton on the way interestingly enough, in fact there was hardly any Vashta Nerada either.

I stopped I guess I must of stopped very suddenly, because the Doctor rammed into me and we tumbled on the ground.

"We're here!" I announced with a smile.

"Great." The Doctor rubbed his head. I trotted over to the access panel an threw it off, breaking the window of the store that was next to me.

I turned to the Doctor "Ready?"

"GERONIMO!" He shouted Jumping into the hole

I laughed, Jumping in after him.

I landing with another impressive survival roll. The bottom of the shaft was dark but There was nothing down there accept for me and the Doctor, who was clearly visible with the 3D glasses, because he was covered in void stuff.

"Okay, landing as a pony is not that easy." He grunted as he got up.

"You okay?"

"Yeah, I'm fine."

I looked around for a light switch "Found it!" The tunnel lights flickered to life. "Ready?"

"Let's do this." We went down the illuminated corridor. It was Quite, a little too quiet. The hum of the generators stopped and the tunnel went pitch black.

"Well I can't see a thing!" I complained.

"Hang on a second." The doctor pulled out his sonic screwdriver and a green light lit up the corridor. "Who turned off the lights?" The Doctor giggled

"What?"

"Nothing."

"Okay." Now the tunnel looked really spooky and dark, completely different than it usually did. "Umm… doctor?"

There were two skeletons, who had presumably been Security guards, Blocked the path in front of us.

" Hello!" The Doctor walked towards them.

"What are you doing?" I asked

**_"You will not pass."_**

"Right, well that doesn't really matter, all I want to do is talk

**_"Trickery!"_**

"No. Now listen, There are clearly millions, no, trillions of you, and what happens if you keep eating ponies? Than there will be more and more of you and eventually you would have wiped a whole planet barren, a planet that could very well have had a bright future, a planet that could have changed this universe, not only that but you would have to find another planet with more lifeforms to eat and eventually there would be nothing to eat and you would all starve, and all of the vashta Nerada would be dead. Now how does that make you feel?"

**_"Well than what do YOU think we should do?"_** The skeleton asked sassily.

"Well…"

I interrupted "The Everfree forest!"

"**_W_**h**_a_**t**_?_**" The Vashta Nerada and the Doctor said at the same time

"The Everfree forest! It's a huge forest just south of here! It's very dark, and you Vashta Nerada could join the food chain in their!"

The three looked at me.

"Pinkie Pie, that is brilliant!" The Doctor turned to the skeletons "It's a win win situation, the Ponies get to live, and you have food! What do you say?"

They thought about it for a second, or they were just silent, either one.

**_"There are millions of us, how do you purpose to convince all of us?"_**

"I convinced you now didn't I?"

**_"We shall proceed to this Everfree forest immediately" _**The skeletons left.

"Theres no more Vashat Nerada in here

"Brilliant! Now Pinkie, we have to get the exact same message across to the rest of the Vashta Nerada before Everyone…"

"Pony" I corrected

"Pony is eaten."

"How?"

"We shout very loudly."

"I like your thinking!"

We made our way back up the ladder, and the sky looked a lot darker.

"Doctor, I can't see town halls roof."

"Their slowly making their way down to the ground, pretty soon we won't be able to see anything!"

"Well than, we'd better start shouting." I grinned "Ready?"

The Doctor grinned back "Let's do this." He turned to the sky "Listen, Vashta Nerada" He paused "And you'd better listen, What we have to say is important for both species, Ponies and Vashta Nerada."

**_"We are listening Doctor."_** The Vashta Nerada sounded like they were everywhere and nowhere all at once, it was creepy.

"Good, There are clearly trillions of you, and If you keep on eating ponies there will be more and more of you, And the more of you there are the more food it will take to feed you all, and eventually you would have destroyed every life-form on this planet, a whole world turned into a desolate wasteland just so you could feed your own bellys? Now to me that sounds like a huge waste, So many innocent lives of ponies that could have done great things, a whole planet bursting with potential, and you would have destroyed it, and once everything on this planet is gone, you'll have to find another planet, then another and another, I've seen this before and the destruction never ends!"

There were a few moments of silence **_"What do you propose? We must eat, everything must eat or it will starve."_**

" Yes I get that! Pinkie had a brilliant idea!"

"Oh, right, well Equestria has lots of woodland, and I mean we are talking, LOTS of woodland, very shaded, lots of different things to eat and you could just join the food chain there, stable food source, you wouldn't have to worry about finding another planet, it's a simple solution!"

**_"Pink Pony, there are more of us than you or the Doctor could count in your lifetimes put together, and you believe that we could fit in a few measly forests?"_**

"Well than some of you could go find another planet, on completely covered in forests, just don't go destroying planets so you can eat!"

**_"But other planets may not have the same energy as here; this energy has made us stronger_**."

"So THAT'S how you've been working together so easily, the unified speaking, the huge cloud, how you all seem to know where were going to be, how you can move around so easily in the skeletons! Of course! Anyways I don't care, this planet is under my protection and I will not let you destroy it!""

They considered this for a moment **_"we were told that you were the only threat to this new food source, and that when you said something was under your protection that you could wipe us out in a few minutes."_**

"By who?" The Doctor seemed caught off guard by this

**_"You have many enemies Doctor, be warned, the Doctor of Discord is coming."_** The veil of Darkness that covered Ponyville broke apart in all different directions, some towards everfree, some up in the sky, some towards other forests.

"What?" The Doctor stood there blinking "That's it? _Oh hey you're serious okay have an ominous riddle bye! _Really?"

"I don't know what to tell you." I sat down next to him "Think they'll cause anymore trouble?"

He shook his head "They shouldn't."

"That's good." Wow. The amount of silence that day was just astounding.

"Well, which way back to that bakery?"

"This way!"

The bakery was extremely messy, not only did it have a huge hole in the floor, but the debris from the crash were everywhere, there were two mangled skeletons on the floor, flour from the day before, muffin crumbs were everywhere eon the table the Doctor had been sitting/sleeping at, and for some reason there were broken plates everywhere.

"So what are you going to do, gonna park your TARDIS on a cloud and let the world pass you by like you planned?"

"Well, it's a whole new universe to explore; I think it's a perfect chance for a new start!"

"So you're going to go around saving more worlds like you did today?"

"It's kind of a normal thing for me. Well than see you!" He walked into his blue box. I stared at the box a bit then went over to the cupboard to get the broom.

"Unless of course, you want to come with me?" The Doctor poked his head out of the TARDIS.

"What?"

"Well, I've kind of missed travelling with someone, or pony or whatever."

" You want me to travel through time and space with you?"

"Yes."

"Oki Doki Loki!" I bounced over there

"So you're coming?"

"Why not? It's a time machine! It's not like we can't come back five minutes after this right? What have I got to lose?"

He beamed "Brilliant! All of time and Space, Where do you want to go first?"

End of Adventure one.

* * *

Authors note:

Sorry that took so long, The next one will be up soon, I will try to find more time to write!


	9. Epilogue

Derpy turned the page. The next page was blank.

"What!" She frowned fluttering through the pages "Nothing!" She was about to throw the book down the alley when she remembered Pinkies note. _Each story should come to you when it needs to. _"Well that's just great! Uh oh, Carrot top is still in the basement." She shoved the journal into her bag and left for her house.

Finding her house was actually quite a feat considering that she had no idea where she was or which way she went to get there, but after a few dead ends and backtracks, she finally got there. Needless to say, Carrot top was furious.

"THAT WAS THE STUPIDIST THING YOU HAVE EVER DONE DERPY, WHAT IF YOU INJURED YOURSELF AND WE WERE TRAPPED DOWN THERE WITH NO FOOD, NO WATER, NOTHING!"

"I left a note…" Derpy pointed out weakly

"THAT ISN'T GOOD ENOUGH, HOW COULD YOU POSSIBLY KNOW THAT SOMEPONY WOULD FIND IT! YOU LOCKED YOUR OWN DAUGHTERS DOWN THERE! YOU ARE A MOTHER, YOU SHOULD BE MORE RESPONSIBLE! I CAN'T GO LOOKING AFTER THEM EVERYTIME YOUR NOT THERE! AND EVEN IF YOU WERE THERE YOU WOULD JUST SCREW IT UP LIKE ALWAYS!"

Sparkler stepped in between the two mares "Carrot top calm down! You're making mom upset!"

"AND SHE SHOULD BE! THERE IS NO PLAUSIBLE REASON TO LOCK SOMEPONY IN THE BASEMENT! WHAT THE HAY WHERE YOU THINKING?"

"There… there is a very good reason I locked you in the basement, I just can't tell you." Derpy sniffed

"AND WHY NOT? YOU PUT US AT RISK WHEN YOU LOCKED US IN THERE AND…"

"CARROT TOP CALM DOWN." Sparkler shouted in a terrifying manner that caused everypony in the room to fall silent "Now I am sure that Mom had a very good reason to lock us in the basement and the only thing you are doing by shouting at her is scaring her and Dinky, So shut up and let her explain!"

"Th… thanks Sparkler. Well, I had to find out what was happening and I didn't want you guys getting hurt so I thought the basement would be safe."

Carrot top sighed "Derpy, that was an incredibly stupid thing to do, promise me yyou will never ever do that again under any circumstances."

"I promise, I'm sorry."

"Alright, now lets have lunch."

Derpy looked in the corner where Dinky was huddled

"Its alright, you can come out now." She lifted the periwinkle unicorns tail of her face "We're going to go out for lunch today, won't that be fun?"

"Carrot Tops not mad at you any more?"

Derpy shook her head "Not at all."

Pinkie Pie skipped into the TARDIS console room.

"This place is Amazing! I mean you have a swimming pool! A SWIMMING POOL!"

"Pretty cool isn't it?"

"Are you kidding! You have everything here!"

The Doctor noticed the red journal in Pinkies hooves "What's that?"

"It's a journal, I thought I could keep a record of all our adventures!

"That's brilliant! Why hasn't that been done before! Wait, never mind, I think I did it once…" Pinkie passed the book, which the doctor dropped almost immediately "How can you hold stuff with thes!?"

"I dunno, I just do. You know what, I don't really know who you are, and you don't know how to use hooves, so your new nickname is whooves!"

" Okay then!" the Doctor smiled, then he froze. "Wait a minute."

"what?"

"You're naked…"

"I guess so."

"ah, would you mind, well putting something on?"

"I don't really have any cloths, you know ponies don't usually wear cloths, we only wear cloths, sometimes."

"The TARDIS has a huge closet I'm sure something would fit a pony!"

"Where is it?"

"Here, I'll show you."

Derpy walked down sugarcube street, where a clean up crew was collecting all of the skeletons. A green unicorn walked over to Derpy and her family

"Derpy Hooves, do you have a moment?"

"Oh sorry I was just about to go to lunch."

Lyra nodded "Right, Listen, I was wondering if you could drop by my place for lunch tomorrow, I'm sure there is much to be discussed."

"I have work tomorrow."

"Right, we'll have our best ponies on it." She turned around and called over a cream earth pony"Hey Bon Bon, we have a pony that needs to be let off work tomorrow, her name is Derpy Hooves and she works at…"

"Equestria postal service"

"I'm on it." she nodded

"Oh um… okay."

"This has the address." Lyra handed Derpy a business card "Twelve o'clock, don't be late."

Derpy looked at it, it read R.I.F.T, research institute for fissures in time, 899 Everfree street.

"Who was that?" Carrot top asked

"Oh, um, that was Lyra, she's a…friend I guess."

"Right, let's get to lunch then."

As Derpy passed Sugarcube corner, she could see the crater the TARDIS left in the bakeries floor. _Where did it go?_ She wondered.

She looked forward again, and barely visible, there was a white Pegasus, she had a yellow mane and despite being the wrong species she looked exactly like Pinkie Pie. She pressed a button on the device that she had on her wrist and disappeared.

_Who was that? _The grey mare wondered, not at all aware of the danger brewing right there in the very town she called home, Equestria had faced many threats before but none like this, The Doctor of Discord was coming...

**The Doctor and Pinkie will return in Doctor Whooves Episode two: the Eggs** from** space.**


End file.
